Research workbench
Crystal structure of chaetomium thermophilum GLE1 ctd-NUP42 gbm-IP6 complex
Analyse Crystal structure of chaetomium thermophilum GLE1 ctd-NUP42 gbm-IP6 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B4H
- Type
- protein
- Length
- 762 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoporin AMO1; Nucleoporin GLE1
- UniProt
- G0S381, G0S7F3
- Ligands
- IHP, ZN
- Pockets
- 11 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Nucleoporin AMO1 | protein | 64 | 38% helix, 0% strand | G0S381 |
| A, C | Nucleoporin GLE1 | protein | 318 | 66% helix, 3% strand | G0S7F3 |
| B | Nucleoporin AMO1 | protein | 62 | 34% helix, 0% strand | G0S381 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 6 copies · chains A, C
- ZN · Zinc ion · metal · 4 copies
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.60 | 0.77 | 36 | empty |
| 2 | 368 | 0.59 | 0.76 | 41 | empty |
| 3 | 345 | 0.56 | 0.75 | 33 | empty |
| 4 | 54 | 0.44 | 0.83 | 16 | empty |
| 5 | 65 | 0.40 | 0.80 | 16 | empty |
Interfaces
3 interfaces between chains.
- D–C · 1180 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1108 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 130 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6B4H · Crystal structure of Chaetomium thermophilum Gle1 CTD-Nup42 GBM-IP6 complex · the same entry in another collection · chain C against C, TM-score 1.00
- G0S7F3 · AlphaFold monomer V2.0 prediction for nucleoporin GLE1 (G0S7F3) · a predicted model of the same protein · chain C against A, TM-score 0.99
- G0S381 · AlphaFold monomer V2.0 prediction for nucleoporin AMO1 (G0S381) · a predicted model of the same protein · chain B against A, TM-score 0.91
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt G0S381
- Every structure of UniProt G0S7F3
- Elsewhere: RCSB PDB 6B4H · PDBe 6B4H · UniProt G0S381 · UniProt G0S7F3
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